[go: up one dir, main page]

EP1960555A4 - METHODS AND SYSTEMS FOR DESIGNING PRIMERS AND PROBES - Google Patents

METHODS AND SYSTEMS FOR DESIGNING PRIMERS AND PROBES

Info

Publication number
EP1960555A4
EP1960555A4 EP06844656A EP06844656A EP1960555A4 EP 1960555 A4 EP1960555 A4 EP 1960555A4 EP 06844656 A EP06844656 A EP 06844656A EP 06844656 A EP06844656 A EP 06844656A EP 1960555 A4 EP1960555 A4 EP 1960555A4
Authority
EP
European Patent Office
Prior art keywords
probes
systems
methods
designing primers
primers
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP06844656A
Other languages
German (de)
French (fr)
Other versions
EP1960555A2 (en
Inventor
James R Hully
Raymond P Lauer
Gilead Kedem
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Intelligent Medical Devices Inc
Original Assignee
Intelligent Medical Devices Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Intelligent Medical Devices Inc filed Critical Intelligent Medical Devices Inc
Publication of EP1960555A2 publication Critical patent/EP1960555A2/en
Publication of EP1960555A4 publication Critical patent/EP1960555A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Analytical Chemistry (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Evolutionary Biology (AREA)
  • Wood Science & Technology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Virology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP06844656A 2005-11-29 2006-11-29 METHODS AND SYSTEMS FOR DESIGNING PRIMERS AND PROBES Withdrawn EP1960555A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US74058205P 2005-11-29 2005-11-29
PCT/US2006/045787 WO2007064758A2 (en) 2005-11-29 2006-11-29 Methods and systems for designing primers and probes

Publications (2)

Publication Number Publication Date
EP1960555A2 EP1960555A2 (en) 2008-08-27
EP1960555A4 true EP1960555A4 (en) 2011-09-07

Family

ID=38092776

Family Applications (1)

Application Number Title Priority Date Filing Date
EP06844656A Withdrawn EP1960555A4 (en) 2005-11-29 2006-11-29 METHODS AND SYSTEMS FOR DESIGNING PRIMERS AND PROBES

Country Status (6)

Country Link
US (1) US20070259337A1 (en)
EP (1) EP1960555A4 (en)
JP (1) JP2009517087A (en)
AU (1) AU2006320541B2 (en)
CA (1) CA2632380A1 (en)
WO (1) WO2007064758A2 (en)

Families Citing this family (59)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7827004B2 (en) * 2006-07-31 2010-11-02 Yahoo! Inc. System and method of identifying and measuring response to user interface design
WO2010048511A1 (en) * 2008-10-24 2010-04-29 Becton, Dickinson And Company Antibiotic susceptibility profiling methods
US20110269138A1 (en) * 2008-12-30 2011-11-03 Qiagen Hamburg Gmbh Method for detecting methicillin-resistant staphylococcus aureus (mrsa) strains
WO2011035322A2 (en) * 2009-09-21 2011-03-24 Intelligent Medical Devices, Inc. Optimized probes and primers and methods of using same for the binding, detection, differentiation, isolation and sequencing of influenza a; influenza b; 2009 inlfuenza a/h1n1; and a 2009 influenza a/h1n1 rna sequence mutation associated with oseltamivir resistance
US20110256535A1 (en) * 2010-02-11 2011-10-20 Intelligent Medical Devices, Inc. Optimized oligonucleotides and methods of using same for the detection, isolation, amplification, quantification, monitoring, screening and sequencing of clostridium difficile genes encoding toxin b, and/or toxin a and/or binary toxin
EP2625297B1 (en) * 2010-10-04 2018-10-10 Gen-Probe Prodesse, Inc. Compositions, methods and kits to detect adenovirus nucleic acids
US8715939B2 (en) * 2011-10-05 2014-05-06 Gen-Probe Incorporated Compositions, methods and kits to detect adenovirus nucleic acids
CA2827429C (en) * 2011-01-19 2020-03-24 Cb Biotechnologies, Inc. Polymerase preference index
WO2013006720A2 (en) * 2011-07-06 2013-01-10 Intelligent Medical Devices, Inc. Optimized probes and primers and methods of using same for the binding, detection, differentiation, isolation and sequencing of influenza a; influenza b and respiratory syncytial virus
AU2013205090B2 (en) * 2012-12-07 2016-07-28 Gen-Probe Incorporated Compositions and Methods for Detecting Gastrointestinal Pathogen Nucleic Acid
US10395777B2 (en) 2014-10-21 2019-08-27 uBiome, Inc. Method and system for characterizing microorganism-associated sleep-related conditions
US10381112B2 (en) 2014-10-21 2019-08-13 uBiome, Inc. Method and system for characterizing allergy-related conditions associated with microorganisms
US10357157B2 (en) 2014-10-21 2019-07-23 uBiome, Inc. Method and system for microbiome-derived characterization, diagnostics and therapeutics for conditions associated with functional features
US11783914B2 (en) 2014-10-21 2023-10-10 Psomagen, Inc. Method and system for panel characterizations
US10777320B2 (en) 2014-10-21 2020-09-15 Psomagen, Inc. Method and system for microbiome-derived diagnostics and therapeutics for mental health associated conditions
US10366793B2 (en) 2014-10-21 2019-07-30 uBiome, Inc. Method and system for characterizing microorganism-related conditions
US9754080B2 (en) 2014-10-21 2017-09-05 uBiome, Inc. Method and system for microbiome-derived characterization, diagnostics and therapeutics for cardiovascular disease conditions
US10265009B2 (en) 2014-10-21 2019-04-23 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for conditions associated with microbiome taxonomic features
US10793907B2 (en) 2014-10-21 2020-10-06 Psomagen, Inc. Method and system for microbiome-derived diagnostics and therapeutics for endocrine system conditions
US10789334B2 (en) 2014-10-21 2020-09-29 Psomagen, Inc. Method and system for microbial pharmacogenomics
US10388407B2 (en) 2014-10-21 2019-08-20 uBiome, Inc. Method and system for characterizing a headache-related condition
US10325685B2 (en) 2014-10-21 2019-06-18 uBiome, Inc. Method and system for characterizing diet-related conditions
US10409955B2 (en) 2014-10-21 2019-09-10 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for locomotor system conditions
US9710606B2 (en) 2014-10-21 2017-07-18 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for neurological health issues
US10073952B2 (en) 2014-10-21 2018-09-11 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for autoimmune system conditions
US10346592B2 (en) 2014-10-21 2019-07-09 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for neurological health issues
US10410749B2 (en) 2014-10-21 2019-09-10 uBiome, Inc. Method and system for microbiome-derived characterization, diagnostics and therapeutics for cutaneous conditions
US10169541B2 (en) 2014-10-21 2019-01-01 uBiome, Inc. Method and systems for characterizing skin related conditions
US10311973B2 (en) 2014-10-21 2019-06-04 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for autoimmune system conditions
US9758839B2 (en) 2014-10-21 2017-09-12 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for conditions associated with microbiome functional features
US9703929B2 (en) 2014-10-21 2017-07-11 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics
US9760676B2 (en) 2014-10-21 2017-09-12 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for endocrine system conditions
CA2968527C (en) * 2014-11-21 2019-01-29 Nantomics, Llc Systems and methods for identification and differentiation of viral infection
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
WO2016100049A1 (en) 2014-12-18 2016-06-23 Edico Genome Corporation Chemically-sensitive field effect transistor
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
US10006910B2 (en) 2014-12-18 2018-06-26 Agilome, Inc. Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9618474B2 (en) 2014-12-18 2017-04-11 Edico Genome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10246753B2 (en) 2015-04-13 2019-04-02 uBiome, Inc. Method and system for characterizing mouth-associated conditions
CN107849599A (en) * 2015-06-30 2018-03-27 优比欧迈公司 method and system for diagnostic test
US10796783B2 (en) 2015-08-18 2020-10-06 Psomagen, Inc. Method and system for multiplex primer design
US11728009B2 (en) * 2016-03-01 2023-08-15 Fusion Genomics Corporation System and process for data-driven design, synthesis, and application of molecular probes
WO2017201081A1 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
WO2017210437A1 (en) * 2016-06-01 2017-12-07 Life Technologies Corporation Methods and systems for designing gene panels
KR102239375B1 (en) * 2016-10-06 2021-04-13 주식회사 씨젠 Method for providing oligonucleotides used for detection of target nucleic acid molecules in samples
EP3601617B3 (en) * 2017-03-24 2024-03-20 Gen-Probe Incorporated Compositions and methods for detecting or quantifying parainfluenza virus
EP4219770A3 (en) * 2017-03-24 2023-08-16 Gen-Probe Incorporated Compositions and methods for detection of rsv b in samples
ES2998109T3 (en) 2017-08-11 2025-02-19 Seegene Inc Methods for preparing oligonucleotides for detecting target nucleic acid sequences with a maximum coverage
KR102084684B1 (en) * 2018-05-15 2020-03-04 주식회사 디나노 A method for designing an artificial base sequence for binding to multiple nucleic acid biomarkers, and multiple nucleic acid probes
US20220148678A1 (en) * 2019-02-28 2022-05-12 Seegene, Inc. Methods for determining a designable region of oligonucleotides
CN110257387B (en) * 2019-07-04 2022-10-28 广西科学院 Aptamer for identifying grass carp hemorrhagic disease virus as well as construction method and application thereof
CN110438258B (en) * 2019-07-22 2021-05-04 中国农业大学 A method for detecting H7N9 subtype avian influenza virus genome vRNA-vRNA interaction using gel migration
AU2020384498A1 (en) * 2019-11-12 2022-06-23 Regeneron Pharmaceuticals, Inc. Methods and systems for identifying, classifying, and/or ranking genetic sequences
CN115101126B (en) * 2022-02-22 2023-04-18 中国医学科学院北京协和医院 Respiratory tract virus and/or bacterial subtype primer design method and system based on CE platform
CN114574634B (en) * 2022-05-06 2022-07-15 山东康华生物医疗科技股份有限公司 Primer probe composition and kit for detecting canine parainfluenza virus, canine adenovirus type II and canine mycoplasma and preparation method thereof
WO2024211706A1 (en) * 2023-04-06 2024-10-10 Detect, Inc. Automated design of primer sets for nucleic acid amplification
CN117683918B (en) * 2023-12-14 2025-09-30 广州达安基因股份有限公司 A digital PCR detection primer and probe combination for Ureaplasma urealyticum and a kit thereof
CN120544659B (en) * 2025-05-12 2026-01-06 粤港澳大湾区精准医学研究院(广州) A primer and probe design method

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001005935A2 (en) * 1999-07-16 2001-01-25 Rosetta Inpharmatics, Inc. Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
US20050250115A1 (en) * 2003-05-07 2005-11-10 Vera Cherepinsky Nucleic acid analysis by multiplexed hybridization and probe design for multiplexed hybridization analysis

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6015664A (en) * 1995-11-03 2000-01-18 Mcw Research Foundation Multiplex PCR assay using unequal primer concentrations to detect HPIV 1,2,3 and RSV A,B and influenza virus A, B
US6482414B1 (en) * 1998-08-13 2002-11-19 The University Of Pittsburgh-Of The Commonwealth System Of Higher Education Cold-adapted equine influenza viruses
US20040081958A1 (en) * 2000-06-07 2004-04-29 Ken Eilertsen Identification and use of molecular markers indicating cellular reprogramming
US20030099974A1 (en) * 2001-07-18 2003-05-29 Millennium Pharmaceuticals, Inc. Novel genes, compositions, kits and methods for identification, assessment, prevention, and therapy of breast cancer
US20050202414A1 (en) * 2001-11-15 2005-09-15 The Regents Of The University Of California Apparatus and methods for detecting a microbe in a sample
EP1473370A3 (en) * 2003-04-24 2005-03-09 BioMerieux, Inc. Genus, group, species and/or strain specific 16S rDNA Sequences

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001005935A2 (en) * 1999-07-16 2001-01-25 Rosetta Inpharmatics, Inc. Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
US20050250115A1 (en) * 2003-05-07 2005-11-10 Vera Cherepinsky Nucleic acid analysis by multiplexed hybridization and probe design for multiplexed hybridization analysis

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
GARDNER SHEA N ET AL: "Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus.", JOURNAL OF CLINICAL MICROBIOLOGY JUN 2003 LNKD- PUBMED:12791858, vol. 41, no. 6, June 2003 (2003-06-01), pages 2417 - 2427, XP002651429, ISSN: 0095-1137 *

Also Published As

Publication number Publication date
CA2632380A1 (en) 2007-06-07
WO2007064758A3 (en) 2009-04-30
EP1960555A2 (en) 2008-08-27
US20070259337A1 (en) 2007-11-08
AU2006320541A1 (en) 2007-06-07
WO2007064758A2 (en) 2007-06-07
AU2006320541B2 (en) 2013-05-23
JP2009517087A (en) 2009-04-30

Similar Documents

Publication Publication Date Title
EP1960555A4 (en) METHODS AND SYSTEMS FOR DESIGNING PRIMERS AND PROBES
GB2453278B (en) Wired drill pipes
ITBO20050495A1 (en) EXOGUE PIPELINE
EP1825528A4 (en) POLE-ZERO ELEMENTS AND ASSOCIATED SYSTEMS AND METHODS
DK1976782T6 (en) SYSTEMS AND METHODS FOR REORIENTATING OBJECTS
EP1751765A4 (en) COMMANDABLE NANO CHEMICAL MEMORY ELEMENT
DE602007004461D1 (en) CLOCK SIGNAL
DK2079485T3 (en) PHENYLPROPIONAMIDE COMPOUNDS AND THE USE THEREOF
DK1907748T3 (en) Pipe
DK2001556T3 (en) Thioninium compounds and their use
ATE513808T1 (en) HETEROARYLPYRROLIDINYL AND PIPERIDINYL KETONE DERIVATIVES
EP1938712A4 (en) INHIBITION DEVICE FOR SEAT
SE0600995L (en) Detector Response Modeling
DE602006010950D1 (en) Magnetoresistive element
EP1952595A4 (en) SYSTEMS AND METHODS FOR PREVENTING COLLISIONS
EP2024953A4 (en) Improved music notation
EP1908005A4 (en) SYSTEMS AND METHODS FOR SALE AND ACQUIRING CONTROL PRIORITY
EP1857814A4 (en) GAS SENSOR
EP1846235A4 (en) METHODS AND SYSTEMS FOR COLLAPTING POLYETHYLENE PIPE
EP2049826A4 (en) PIPELINE
EP1887325A4 (en) METER
EP2109863A4 (en) REVERSIBLE POLARITE DECODER CIRCUIT, AND ASSOCIATED METHODS
GB0613902D0 (en) Scale and readhead
DE112006002175A5 (en) Well Pipe
FI20050052A0 (en) Method and arrangement for chemical recovery boiler

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

17P Request for examination filed

Effective date: 20080627

AK Designated contracting states

Kind code of ref document: A2

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI SK TR

AX Request for extension of the european patent

Extension state: AL BA HR MK RS

RIN1 Information on inventor provided before grant (corrected)

Inventor name: KEDEM, GILEAD

Inventor name: LAUER, RAYMOND, P.

Inventor name: HULLY, JAMES, R.

R17D Deferred search report published (corrected)

Effective date: 20090430

RIC1 Information provided on ipc code assigned before grant

Ipc: C07H 21/04 20060101AFI20090520BHEP

RIC1 Information provided on ipc code assigned before grant

Ipc: C07H 21/04 20060101ALI20110728BHEP

Ipc: G06F 19/00 20110101AFI20110728BHEP

A4 Supplementary search report drawn up and despatched

Effective date: 20110809

DAX Request for extension of the european patent (deleted)
STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20140603